Contacts of the helix formed by residues 68 - 79 (chain B) in PDB entry 2N5E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A HIS* 3.9 31.9 + - + +
64B LEU* 5.1 3.1 - - + +
65B GLY 2.9 25.6 - - - +
67B VAL* 1.3 85.2 - - - +
69B GLN* 1.3 76.5 + - + +
71B PHE* 3.2 18.0 + - - +
72B TRP* 3.1 23.4 + - + +
240B LEU* 6.3 2.2 - - - -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 3.6 25.2 + - - +
64B LEU* 3.7 24.2 - - - +
65B GLY 4.6 0.4 + - - -
66B PRO* 2.9 26.2 + - - +
68B THR* 1.3 87.1 - - + +
70B GLU* 1.3 57.8 + - - +
72B TRP* 3.1 20.3 + - + +
73B ASP* 2.9 33.0 + - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PRO 3.5 5.6 + - - +
67B VAL* 3.2 10.3 + - - +
69B GLN* 1.3 76.6 - - - +
71B PHE* 1.3 61.1 - - + +
73B ASP* 4.0 9.2 - - - +
74B ASN* 2.7 50.0 + - + +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 2.8 43.3 + - + -
68B THR* 3.2 15.5 - - - +
69B GLN 3.1 0.2 - - - -
70B GLU* 1.3 80.0 - - + +
72B TRP* 1.3 58.4 + - - +
74B ASN* 4.1 1.5 - - - +
75B LEU* 3.0 32.8 + - - +
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Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY* 5.8 6.1 - - - -
189A LEU* 4.5 26.0 - - + -
190A ALA* 6.3 3.1 - - + +
68B THR* 3.1 27.5 + - + +
69B GLN* 3.1 26.6 + - + +
71B PHE* 1.3 77.7 - - - +
73B ASP* 1.3 81.7 + - + +
75B LEU* 4.4 6.0 - - - +
76B GLU* 2.9 50.1 + - + +
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLN 2.9 23.5 + - - +
70B GLU* 3.9 7.7 - - - +
72B TRP* 1.3 102.7 - - + +
74B ASN* 1.3 64.9 + - - +
76B GLU* 4.1 0.9 - - - +
77B LYS* 2.8 43.5 + - - +
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU* 2.7 37.1 + - + +
71B PHE* 4.1 1.6 - - - +
73B ASP* 1.3 78.7 + - - +
75B LEU* 1.3 62.8 + - - +
77B LYS* 3.3 13.1 + - - +
78B GLU* 3.1 34.9 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 6.4 0.4 - - - +
189A LEU* 5.7 8.5 - - + -
71B PHE 3.0 21.3 + - - +
72B TRP* 4.0 5.4 - - - +
74B ASN* 1.3 76.7 - - - +
76B GLU* 1.3 54.6 + - + +
78B GLU* 3.2 5.4 + - - +
79B THR* 2.6 50.5 + - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 3.3 31.3 + - - +
186A GLY* 4.7 16.3 + - - -
189A LEU* 5.7 3.8 - - - +
72B TRP* 2.9 39.6 + - + +
73B ASP 4.1 1.8 - - - +
75B LEU* 1.3 77.8 - - + +
77B LYS* 1.3 62.1 + - - +
79B THR* 3.8 10.4 - - - +
80B GLU* 3.0 37.1 + - - +
82B LEU* 5.2 0.3 - - - +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASP* 2.8 31.8 + - - +
74B ASN* 3.3 14.8 - - - +
75B LEU 3.1 0.2 - - - -
76B GLU* 1.3 79.8 - - - +
78B GLU* 1.3 70.7 + - - +
80B GLU* 3.3 22.6 - - - +
81B GLY 4.6 0.3 + - - -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN* 3.1 23.4 + - - +
75B LEU* 3.9 3.4 - - - +
77B LYS* 1.3 85.2 - - - +
79B THR* 1.3 65.3 + - - +
80B GLU 3.1 3.5 + - - -
81B GLY* 3.2 13.3 + - - -
82B LEU 4.7 0.2 + - - -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 3.9 10.8 - - - +
75B LEU* 2.6 39.6 + - + +
76B GLU* 3.3 19.0 + - - +
78B GLU* 1.3 74.9 - - - +
80B GLU* 1.3 66.1 + - - +
81B GLY 3.0 0.2 - - - -
82B LEU* 2.8 43.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il